Center for Complex Biological Systems
GPU Codes for 3D Modeling
3D model, GPU code, intracellular network, cell growth, division
Qing Nie
http://cmcb.math.uci.edu/GPU3D.html
SysBioCenters
Provides CUDA code for Nvidia GPUs of a 3D model of epidermal development. The model includes GPU implementation of the subcellular element method for 3D spatial cells, an intracellular gene network for each cell represented by a set of ODEs, cell-cell neighbor communication through Notch signaling as part of each cell's internal gene network, and cell behaviors of growth and division.
qnie@math.uci.edu
University of California Irvine
doi:10.1016/j.jcp.2005.09.030
Felix Grun
University of California
Center for Complex Biological Systems
doi:10.1016/j.jcp.2008.01.05
http://cmcb.math.uci.edu/stiffsolvers.html
numerical algorithms, reaction-diffusion, spatial dynamics
Fast Numerical Algorithms for Stiff Reaction-Diffusion Equations. Provdies Matlab and C codes based on a novel and efficient algorithm for Reaction-Diffusion equations that model spatial dynamics of complex biological systems. The numerical method used in the code is designed for effective treatment of stiff reactions in spatial systems.
Stiff Reaction Diffusion Solvers
Qing Nie
qnie@math.uci.edu
SysBioCenters
SysBioCenters
Sigmoid
Eric Mjolsness
University of California Irvine
emj@uci.edu
PMCID: PMC3021415
http://www.sigmoid.org/home/
Center for Complex Biological Systems
Felix Grun
The SIGMOID project is intended to produce a database of cellular signaling pathways and models thereof, to marshall the major forms of data and knowledge required as input to cellular modeling software and also to organize the outputs.
PMID: 20865537
http://ccbs.uci.edu/
kymartin@uci.edu
Karen Martin
A monthly seminar series for CCBS-affiliated scientists with interests in Systems Biology. The seminars are presented by a mix of local and outside speakers.
seminar series, systems biology
Systems Biology Seminar Series
University of California Irvine
Center for Complex Biological Systems
SysBioCenters
Center for Complex Biological Systems
Eric Mjolsness
SysBioCenters
http://computableplant.ics.uci.edu/erleap/
Accelerated Stochastic Simulation Algorithm for Reaction Networks
University of California Irvine
stochastic simulation, chemical reaction networks
This is an exact method for stochastic simulation of chemical reaction networks (Exact R-Leap) to accelerate the Stochastic Simulation Algorithm (SSA).
emj@uci.edu
Plenum Dynamical Grammar Simulator
University of California Irvine
emj@uci.edu
http://computableplant.ics.uci.edu/theses/guy/Plenum.html
dynamical grammar, stochastic, Mathematica
Eric Mjolsness
SysBioCenters
Plenum is a simulation software written in Mathematica for dynamical grammar models. Dynamical grammars are an elegant language for representing complex processes that include stochastic events and continuous dynamics.
Center for Complex Biological Systems
SysBioCenters
Center for Complex Biological Systems
University of California Irvine
systems biology, short course, morphogenesis, spatial dynamics, videos, lectures
National Short Course on Systems Biology of Morphogenesis and Spatial Dynamics
fgrun@uci.edu
(949) 824-6432
Felix Grun
This national short course in Systems Biology explores the themes of Morphogenesis and Spatial Dynamics. The course consists of lectures, wet bench experimentation and hands-on modeling and is designed for graduate students, postdocs and faculty/industry researchers with little or no formal training in systems biology. The course is held at UCI annually each January. Videos/notes of course lectures are available from the website.
http://ccbs.uci.edu/nscsbhome
University of California Irvine
Center for Complex Biological Systems
http://computableplant.ics.uci.edu/sw.html
modeling, image analysis, systems inference tools
A collection of software and packages for modeling and image analysis on systems inferences.
SysBioCenters
emj@uci.edu
Eric Mjolsness
Scientific Inference Systems Tools
Center for Complex Biological Systems
seminar series, microscopy
Working group to discuss research advances and applications related to correlation techniques in advanced microscopy imaging tools.
Felix Grun
SysBioCenters
Advanced Correlation Techniques Group
Michelle Digman
mdigman@uci.edu
University of California Irvine
http://www.lfd.uci.edu/
University of California Irvine
http://bioweb.bio.uci.edu/sgross/
Automated Particle Tracking and Analysis
sgross@uci.edu
Steve Gross
SysBioCenters
Center for Complex Biological Systems
A LabView module to allow particle tracking in time-stack images.
particle tracking, LabView
spectroscopic software tools
University of California
Tracey Scott
Laboratory for Fluorescence Imaging
Felix Grun
Software analysis tools for image files derived from multiple spectroscopic techniques.
Globals for Images
SysBioCenters
tscott1@uci.edu
http://www.lfd.uci.edu/globals/
qnie@math.uci.edu
Felix Grun
Gene Network Inference
PMID: 19710931
Provides Objective-C (Cocoa for Mac, GNUstep for Linux/Windows) optimization framework to learn linear gene regulatory networks from various types of gene expression data. The optimization incorporates network sparsity constraint through L1 regularization as well as incorporation of existing network information. The framework can handle wild type, perturbation, gene knockout and heterozygous knockdown gene expression data.
Center for Complex Biological Systems
http://cmcb.math.uci.edu/genenetwork.html
University of California Irvine
Qing Nie
SysBioCenters
gene regulatory networks, expression data
Enrico Gratton
Laboratory of Fluorescence Dynamics
The Laboratory for Fluorescence Dynamics (LFD) is a national research resource center for biomedical fluorescence spectroscopy. The LFD's main activities are i) Services and Resources for state-of-the-art fluorescence measurements, microscopy and spectroscopy, ii) Research and Development to design, test, and implement advances in the technology of hardware, software, and biomedical application, and iii) Training and Dissemination of knowledge relevant to fluorescence spectroscopic principles, instrumentation, and applications.
lfd@uci.edu
Felix Grun
University of California Irvine
SysBioCenters
fluorescence mircoscopy applications, instrumentation, training
Center for Complex Biological Systems
http://www.lfd.uci.edu/